OnWorks favicon

bp_taxonomy2treep - Online in the Cloud

Run bp_taxonomy2treep in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command bp_taxonomy2treep that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator



bp_taxonomy2tree - Building a taxonomic tree based on the full lineages of a set of
species names


This scripts looks up the provided species names in the NCBI Taxonomy database, retrieves
their full lineage and puts them in a Newick taxonomic tree displayed on screen.

bp_taxonomy2tree.pl -s Orangutan -s Gorilla -s Chimpanzee -s Human
bp_taxonomy2tree.pl -s Orangutan -s Gorilla -s Chimpanzee -s "Homo Sapiens"

Can also provide -d to specify the directory to store index files in, -o to specify the
location of your NCBI nodes file, and -a for the NCBI names file. Or the option -e to use
the web-based Entrez taxonomy database if you do not have the NCBI flatfiles installed.

This script requires that the bioperl-run pkg be also installed.

Providing the nodes.dmp and names.dmp files from the NCBI Taxonomy dump (see
Bio::DB::Taxonomy::flatfile for more info) is only necessary on the first time running.
This will create the local indexes and may take quite a long time. However once created,
these indexes will allow fast access for species to taxon id OR taxon id to species name

AUTHOR - Gabriel Valiente, reimplemented by Sendu Bala

Email [email protected] Email [email protected]

Use bp_taxonomy2treep online using onworks.net services

Free Servers & Workstations

Download Windows & Linux apps

  • 1
    Eclipse Tomcat Plugin
    Eclipse Tomcat Plugin
    The Eclipse Tomcat Plugin provides
    simple integration of a tomcat servlet
    container for the development of java
    web applications. You can join us for
    Download Eclipse Tomcat Plugin
  • 2
    WebTorrent Desktop
    WebTorrent Desktop
    WebTorrent Desktop is for streaming
    torrents on Mac, Windows or Linux. It
    connects to both BitTorrent and
    WebTorrent peers. Now there's no
    need to wait for...
    Download WebTorrent Desktop
  • 3
    GenX is a scientific program to refine
    x-ray refelcetivity, neutron
    reflectivity and surface x-ray
    diffraction data using the differential
    evolution algorithm....
    Download GenX
  • 4
    PSPP is a program for statistical
    analysis of sampled data. It is a free
    replacement for the proprietary program
    SPSS. PSPP has both text-based and
    graphical us...
    Download pspp4windows
  • 5
    Git Extensions
    Git Extensions
    Git Extensions is a standalone UI tool
    for managing Git repositories. It also
    integrates with Windows Explorer and
    Microsoft Visual Studio
    (2015/2017/2019). Th...
    Download Git Extensions
  • 6
    eSpeak: speech synthesis
    eSpeak: speech synthesis
    Text to Speech engine for English and
    many other languages. Compact size with
    clear but artificial pronunciation.
    Available as a command-line program with
    many ...
    Download eSpeak: speech synthesis
  • More »

Linux commands